mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
a85c24286b
* Began implementing geometric functions on points * Started common implementation of point functions * Completed implementation of point functions for CustomCompoundBondForce * Implemented point functions for CustomCentroidBondForce * Implemented point functions for CustomManyParticleForce * Use point functions to simplify implementation of custom forces * Removed unnecessary code * Fixed typo
150 lines
6.3 KiB
C++
150 lines
6.3 KiB
C++
/* Portions copyright (c) 2009-2021 Stanford University and Simbios.
|
|
* Contributors: Peter Eastman
|
|
*
|
|
* Permission is hereby granted, free of charge, to any person obtaining
|
|
* a copy of this software and associated documentation files (the
|
|
* "Software"), to deal in the Software without restriction, including
|
|
* without limitation the rights to use, copy, modify, merge, publish,
|
|
* distribute, sublicense, and/or sell copies of the Software, and to
|
|
* permit persons to whom the Software is furnished to do so, subject
|
|
* to the following conditions:
|
|
*
|
|
* The above copyright notice and this permission notice shall be included
|
|
* in all copies or substantial portions of the Software.
|
|
*
|
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
|
|
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
|
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
|
|
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
|
|
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
|
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
|
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
|
*/
|
|
|
|
#ifndef __ReferenceCustomManyParticleIxn_H__
|
|
#define __ReferenceCustomManyParticleIxn_H__
|
|
|
|
#include "ReferenceBondIxn.h"
|
|
#include "openmm/CustomManyParticleForce.h"
|
|
#include "lepton/ExpressionProgram.h"
|
|
#include "lepton/ParsedExpression.h"
|
|
#include <map>
|
|
#include <set>
|
|
#include <vector>
|
|
|
|
namespace OpenMM {
|
|
|
|
class ReferenceCustomManyParticleIxn {
|
|
|
|
private:
|
|
|
|
class ParticleTermInfo;
|
|
int numParticlesPerSet, numPerParticleParameters, numTypes;
|
|
bool useCutoff, usePeriodic, centralParticleMode;
|
|
double cutoffDistance;
|
|
OpenMM::Vec3* periodicBoxVectors;
|
|
Lepton::ExpressionProgram energyExpression;
|
|
std::vector<std::vector<std::string> > particleParamNames;
|
|
std::vector<std::set<int> > exclusions;
|
|
std::vector<int> particleTypes;
|
|
std::vector<int> orderIndex;
|
|
std::vector<std::vector<int> > particleOrder;
|
|
std::vector<ParticleTermInfo> particleTerms;
|
|
|
|
void loopOverInteractions(std::vector<int>& particles, int loopIndex, std::vector<OpenMM::Vec3>& atomCoordinates,
|
|
std::vector<std::vector<double> >& particleParameters, std::map<std::string, double>& variables,
|
|
std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Calculate custom interaction for one set of particles
|
|
|
|
@param particles the indices of the particles
|
|
@param atomCoordinates atom coordinates
|
|
@param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
|
|
@param variables the values of variables that may appear in expressions
|
|
@param forces force array (forces added)
|
|
@param totalEnergy total energy
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
void calculateOneIxn(const std::vector<int>& particles, std::vector<OpenMM::Vec3>& atomCoordinates,
|
|
std::vector<std::vector<double> >& particleParameters, std::map<std::string, double>& variables,
|
|
std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;
|
|
|
|
void computeDelta(int atom1, int atom2, double* delta, std::vector<OpenMM::Vec3>& atomCoordinates) const;
|
|
|
|
static double computeAngle(double* vec1, double* vec2);
|
|
|
|
|
|
public:
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Constructor
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
ReferenceCustomManyParticleIxn(const OpenMM::CustomManyParticleForce& force);
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Destructor
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
~ReferenceCustomManyParticleIxn();
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Set the force to use a cutoff.
|
|
|
|
@param distance the cutoff distance
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
void setUseCutoff(double distance);
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Set the force to use periodic boundary conditions. This requires that a cutoff has
|
|
already been set, and the smallest side of the periodic box is at least twice the cutoff
|
|
distance.
|
|
|
|
@param vectors the vectors defining the periodic box
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
void setPeriodic(OpenMM::Vec3* vectors);
|
|
|
|
/**---------------------------------------------------------------------------------------
|
|
|
|
Calculate the interaction
|
|
|
|
@param atomCoordinates atom coordinates
|
|
@param particleParameters particle parameter values (particleParameters[particleIndex][parameterIndex])
|
|
@param globalParameters the values of global parameters
|
|
@param forces force array (forces added)
|
|
@param totalEnergy total energy
|
|
|
|
--------------------------------------------------------------------------------------- */
|
|
|
|
void calculateIxn(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<std::vector<double> >& particleParameters,
|
|
const std::map<std::string, double>& globalParameters,
|
|
std::vector<OpenMM::Vec3>& forces, double* totalEnergy) const;
|
|
};
|
|
|
|
class ReferenceCustomManyParticleIxn::ParticleTermInfo {
|
|
public:
|
|
std::string name;
|
|
int atom, component;
|
|
Lepton::ExpressionProgram forceExpression;
|
|
ParticleTermInfo(const std::string& name, int atom, int component, const Lepton::ExpressionProgram& forceExpression) :
|
|
name(name), atom(atom), component(component), forceExpression(forceExpression) {
|
|
}
|
|
};
|
|
|
|
} // namespace OpenMM
|
|
|
|
#endif // __ReferenceCustomManyParticleIxn_H__
|